carray 1.3.6 → 1.5.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/.yardopts

@@ -0,0 +1,32 @@
+--markup markdown
+--markup-provider kramdown
+--no-private
+--exclude lib/carray/obsolete.rb
+--exclude lib/carray/autoload.rb
+--exclude 'lib/carray/autoload/'
+--readme README.md
+--files NEWS.md,TODO.md 
+lib/carray.rb 
+ext/ruby_carray.c 
+ext/ca_obj_array.c 
+ext/ca_obj_bitarray.c 
+ext/ca_obj_bitfield.c 
+ext/ca_obj_block.c 
+ext/carray_attribute.c 
+ext/carray_call_cfunc.c 
+ext/carray_cast.c 
+ext/carray_class.c 
+ext/carray_conversion.c 
+ext/carray_copy.c 
+ext/carray_core.c 
+ext/carray_data_type.c 
+ext/carray_element.c 
+ext/carray_generate.c 
+ext/carray_loop.c
+ext/carray_mask.c 
+ext/carray_operator.c 
+ext/carray_order.c 
+ext/carray_sort_addr.c 
+ext/carray_test.c 
+ext/carray_utils.c 
+

data/LICENSE

@@ -0,0 +1,22 @@
+Copyright (c) 2020 Hiroki Motoyoshi.
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/NEWS.md

@@ -0,0 +1,65 @@
+ChangeLog of Ruby/CArray
+========================
+
+1.5.2 -> 1.5.3
+--------------
+
+* [New] Add new method 'CArray#exp2'
+* [New] Add new method 'CArray#log2'
+* [New] Add new method 'CArray#logb'
+* [New] Add new method 'CArray#remainder'
+* [New] Add new method 'CArray.guard_undef'
+* [New] Add new method 'CArray#data_class='
+* [New] Add new method 'CArray.data_class?'
+* [Mod] Modify 'CArray#pmax' to use 'fmax' for float type
+* [Mod] Modify 'CArray#pmin' to use 'fmin' for float type
+* [Mod] Remove method 'Object#undef?'
+* [Mod] Remove method '::nan', '::inf'
+* [Mod] Remove method 'TrueClass#*', 'FalseClass#*' (unknown origin)
+* [Fix] Fix invalid access for CAUnboundRepeat using index
+* [Fix] Fix treatment of extra :* in operation between CAUnboundRepeat objects
+* [Fix] Fix to accept Symbol for the name of data_class member
+* [Fix] Fix 'CArray#uniq' to accept the array with the dimension more than 2.
+* [Fix] Fix for CArray serialization to include data_class
+* [Fix] Fix data_class inheritance in some methods in which new CArray is created.
+* [Fix] Fix 'CArray#broadcast_to' to accept the case of dimension extension.
+
+1.5.1 -> 1.5.2
+--------------
+
+* [New] Add new method 'CArray#sorted_with'
+* [New] Add new method 'CArray#sort_with'
+* [New] Add new method 'CArray#max_with'
+* [New] Add new method 'CArray#min_with'
+* [New] Add new method 'CArray.broadcast'
+* [New] Add new method 'CArray#broadcast_to', 'CScalar#broadcast_to'
+* [New] Add new API function `rb_ca_wrap_new`
+* [Mod] Modify 'CArray#linspace' to return float64 array for integer arguments
+* [Mod] Modify CAUnboundRepeat to have `ndim` same as the bounded array (before `ndim` same as parent array)
+* [Mod] Remove the obsolete mothod 'CArray#dump'.
+* [Mod] Remove the obsolete mothod 'CArray#load'.
+* [Mod] Modify CArray.wrap_readonly to wrap string as array.
+* [Fix] Add support for Integer (same as for Fixnum, Bignum)
+
+1.5.0 -> 1.5.1
+--------------
+
+* [New] Add data type classes like 'Float64' ... to provide the methods like 'CArray::Float64.linspace'
+* [Mod] Modify 'CArray.float64' ... without aruguments to return the corresponding data type class 
+* [Mod] Set obsolete flag to 'CAIterator#sort_with'
+* [Fix] Move C extension files into 'ext/'
+* [Fix] Rename member 'rank' to 'ndim' in struct CArray in C extension
+* [Fix] Remove 'CArray#shuffle' (gone to 'carray-random' gem)
+* [Fix] Remove dependencies on 'rb_secure()' and 'rb_safe_level()'
+* [Fix] Modify 'CArray#span' to handle fractional step for integer array
+
+1.4.0 -> 1.5.0
+--------------
+
+* [Mod] Remove 'Carray#random!' (gone to 'carray-random' gem)
+* [Mod] Relocate file 'lib/carray/io/table.rb' to 'lib/carray/table.rb'
+* [Mod] Rename class 'CA::TableMethods' to 'CArray::TableMethods'
+* [Mod] Rename method 'CArray#cast_other' to 'CArray#cast_with'
+* [Mod] Change license from "Ruby's" to "MIT"
+* [Mod] Remove files 'COPYING', 'LEGAL'(for MT), 'GPL'
+* [Fix] Fix bug lib/carray/struct.rb

data/README.md

@@ -3,41 +3,38 @@ Ruby/CArray
 
 Ruby/CArray is an extension library for the multi-dimensional array class.
 
+Features
+--------
+
+* Multidimensional array for storing uniform data
+* Various ways to access data elements
+* Masks for each element to handle missing values
+* Element-wise operations and mathematical functions
+* Statistical functions for the elements
+* Indirect data manipulation for original array by virtual array 
+* Special iterators (dimension, block, window, categorical)
+* User-defined array
+* Storing fixed length data with data_class
+* Memory sharing with other objects (Experimental)
+
 Requirements
 ------------
 
-* Ruby 2.2.0 or later
+* Ruby 2.4.0 or later
 * C compiler 
   + IEEE754 floating point number
   + C99 complex number
-* Optionally required gems
-  + narray
-  + narray_miss
-  + axlsx
-  + spreadsheet
-  + sqlite3
-* Optional command
-  + Gnuplot
-  + ImageMagick (stream, convert, display, identify)
 
 Directories
 -----------
 
-    .         - Ruby/CArray extension source codes
-    lib       - Ruby/CArray standard library in Ruby
-    ext       - optional extension libraries for Ruby/CArray
-    examples  - some examples
-    test      - some unit tests (incomplete)
-    spec      - some rspec (incomplete)
-    utils     - support tools for development.
-
-Author
-------
-
-Hiroki Motoyoshi 
+    lib       - Ruby sorce codes
+    ext       - C extension source codes
+    utils     - support tools for development
+    spec      - rspec files
+    misc      - misc files
 
-Copying
--------
+Licenses
+--------
 
-You can redistribute this library package and/or modify it under the terms of
-the Ruby Licence. See the file 'COPYING' in this directory.
+MIT (after version 1.5.0)

data/Rakefile

@@ -2,12 +2,43 @@
 #
 #
 
+GEMSPEC = "carray.gemspec"
+
+task :install do
+  spec = eval File.read(GEMSPEC)
+  version_h = `ruby ext/version.rb`.chomp
+  if spec.version.to_s != version_h
+    STDERR.puts "Mismatch in version between carray.gemspec and version.h"
+    STDERR.puts "  carray.gemspec - #{spec.version.to_s }"
+    STDERR.puts "  version.h      - #{version_h}"
+    STDERR.puts "Please check!"
+    exit(1)
+  end
+  system %{
+    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem --no-document
+  }
+end
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new
+
+
+__END__
 require 'rake'
 require 'rake/testtask'
 require 'rspec/core/rake_task'
 
 task :default => :test
 
+GEMSPEC = "carray.gemspec"
+
+task :install do
+  spec = eval File.read(GEMSPEC)
+  system %{
+    gem build #{GEMSPEC}; gem install #{spec.full_name}.gem
+  }
+end
+
 desc "Run the tests"
 Rake::TestTask::new(:test) do |t|
   t.test_files = FileList['test/test_ALL.rb']

data/TODO.md

@@ -0,0 +1,17 @@
+ToDo List
+=========
+
+ToDo
+-------
+ * Implement CArray.broadcast in C
+ * Implement Integer#{|,&,^,<<,>>} with Refinement (remove monkey patch)
+ * Remove RSTRUCT hack in carray_access.c for handling of Range object.
+ * Solve abs probrems
+ * Create spec
+   - str_format (cyclic format)
+   - CA_SIZE
+   - serialization of carray which has data_class
+
+Done
+-------
+

data/carray.gemspec

@@ -1,44 +1,37 @@
-
-
 Gem::Specification::new do |s|
-  require_relative "./version"
-  
-  version, date = carray_version()
 
-  files = Dir.glob("**/*") - [ 
-                            Dir.glob("vendor"),
-                            Dir.glob("ext/**/{Makefile,mkmf.log}"),
-                            Dir.glob("**/*.{o,so,bundle}"),
-                            Dir.glob("**/*~"),
-                            Dir.glob("carray-*.gem"), 
-                           ].flatten
+  version = "1.5.3"
+
+  files = Dir.glob("**/*") + [".yardopts"] -
+                             [ 
+                               Dir.glob("carray-*.gem"), 
+                               Dir.glob("ext/**/{Makefile,mkmf.log}"),
+                               Dir.glob("**/*.{o,so,bundle}"),
+                               Dir.glob("**/*~"),
+                               Dir.glob("doc/**/*"),
+                               Dir.glob("test/**/*"),
+                             ].flatten
 
   s.platform    = Gem::Platform::RUBY
   s.name        = "carray"
-  s.summary     = "Multi-dimesional array class"
+  s.summary     = "Multi-dimesional array class for Ruby"
   s.description = <<-HERE
-    CArray is a uniform multi-dimensional rectangular array class.
-    It provides the various types of sub-arrays and references
-    pointing the data elements of original array (slice, grid, selection ...).
-    Element-wise masking and mathematical operations are natively supported.
+    Ruby/CArray is an extension library for the multi-dimensional numerical array class.
+    CArray can store integers and floating point numbers to perform calculations
+    efficiently. Therefore, Ruby/CArray is suitable for numerical computation and data
+    analysis. Ruby/CArray has different features from other multidimensional array
+    libraries (narray, numo-narray, nmatrix), such as element-wise masks, 
+    creation of reference arrays that can reflect changes to the referent, 
+    the ability to access memory pointers of other objects, user-defined arrays,
+    and so on.
   HERE
   s.version     = version
   s.author      = "Hiroki Motoyoshi"
   s.email       = ""
+  s.license     = 'MIT'
   s.homepage    = 'https://github.com/himotoyoshi/carray'
   s.files       = files
-  s.extensions  = [ "extconf.rb" ] + 
-                     Dir["ext/*/extconf.rb"].select{|f| File.exist?(f) }
-  s.rdoc_options = [
-		"-m rdoc_main.rb", 
-		"rdoc_main.rb", 
-		"rdoc_ext.rb",
-		"rdoc_math.rb", 
-		"rdoc_stat.rb", 
-		Dir.glob("lib/carray/**/*.rb"),
-	].flatten
-  s.required_ruby_version = ">= 1.8.1"
-  s.add_runtime_dependency 'narray', '~> 0.6.1.1'
-  s.add_runtime_dependency 'narray_miss', '~> 1.3'
-  s.add_runtime_dependency 'sqlite3', '~> 1.3'
+  s.extensions  = [ "ext/extconf.rb" ] 
+  s.required_ruby_version = ">= 2.4.0"
 end
+

data/{ca_iter_block.c → ext/ca_iter_block.c}

@@ -3,16 +3,14 @@
   ca_iter_block.c
 
   This file is part of Ruby/CArray extension library.
-  You can redistribute it and/or modify it under the terms of
-  the Ruby Licence.
 
-  Copyright (C) 2005 Hiroki Motoyoshi
+  Copyright (C) 2005-2020 Hiroki Motoyoshi
 
 ---------------------------------------------------------------------------- */
 
 #include "carray.h"
 
-/* rdoc:
+/* yard:
   class CABlockIterator < CAIterator # :nodoc: 
   end
 */
@@ -23,7 +21,7 @@ VALUE rb_cCABlockIterator;
 typedef struct {
   int16_t   obj_type;
   int8_t    data_type;
-  int8_t    rank;
+  int8_t    ndim;
   int32_t   flags;
   ca_size_t   bytes;
   ca_size_t   elements;
@@ -42,11 +40,11 @@ typedef struct {
   ca_size_t  *step;
   ca_size_t  *count;
   ca_size_t  *size0;
-} CABlock;                  // 68 + 20*(rank) (bytes) 
+} CABlock;                  // 68 + 20*(ndim) (bytes) 
 */
 
 typedef struct {
-  int8_t  rank;
+  int8_t  ndim;
   ca_size_t dim[CA_RANK_MAX];
   CArray *reference;
   CArray * (*kernel_at_addr)(void *, ca_size_t, CArray *);
@@ -73,14 +71,14 @@ ca_bi_kernel_at_index (void *it, ca_size_t *idx, CArray *ref)
   else {
     CABlock *ck = (CABlock *)bit->kernel;
     kernel = ca_block_new(ref,
-                          ck->rank, ck->size0,
+                          ck->ndim, ck->size0,
                           ck->start, ck->step, ck->count,
                           ck->offset);
   }
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, bit->dim[i]);
     kernel->start[i] += j * kernel->dim[i];
@@ -99,7 +97,7 @@ ca_bi_kernel_at_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = bit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=bit->rank-1; i>=0; i--) {
+  for (i=bit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -117,7 +115,7 @@ ca_bi_kernel_move_to_index (void *it, ca_size_t *idx, CArray *kern)
 
   ca_update_mask(kernel);
 
-  for (i=0; i<kernel->rank; i++) {
+  for (i=0; i<kernel->ndim; i++) {
     j = idx[i];
     CA_CHECK_INDEX(j, bit->dim[i]);
     kernel->start[i] = j * kernel->dim[i];
@@ -136,7 +134,7 @@ ca_bi_kernel_move_to_addr (void *it, ca_size_t addr, CArray *ref)
   ca_size_t *dim = bit->dim;
   ca_size_t idx[CA_RANK_MAX];
   int8_t i;
-  for (i=bit->rank-1; i>=0; i--) {
+  for (i=bit->ndim-1; i>=0; i--) {
     idx[i] = addr % dim[i];
     addr  /= dim[i];
   }
@@ -158,11 +156,11 @@ ca_bi_setup (VALUE self, VALUE rref, VALUE rker)
   Data_Get_Struct(rref, CArray, ref);
   Data_Get_Struct(rker, CABlock, ker);
 
-  if ( ref->rank != ker->rank ) {
-    rb_raise(rb_eRuntimeError, "rank mismatch between reference and kernel");
+  if ( ref->ndim != ker->ndim ) {
+    rb_raise(rb_eRuntimeError, "ndim mismatch between reference and kernel");
   }
 
-  for (i=0; i<ref->rank; i++) {
+  for (i=0; i<ref->ndim; i++) {
     if ( ker->step[i] != 1 ) {
       rb_raise(rb_eRuntimeError, "block should be contiguous");
     }
@@ -174,8 +172,8 @@ ca_bi_setup (VALUE self, VALUE rref, VALUE rker)
     */
   }
 
-  it->rank      = ref->rank;
-  memcpy(it->dim, dim, it->rank * sizeof(ca_size_t));
+  it->ndim      = ref->ndim;
+  memcpy(it->dim, dim, it->ndim * sizeof(ca_size_t));
   it->reference = ref;
   it->kernel    = ker;
   it->kernel_at_addr  = ca_bi_kernel_at_addr;
@@ -202,7 +200,7 @@ rb_bi_initialize_copy (VALUE self, VALUE other)
   return self;
 }
 
-/* rdoc:
+/* yard:
   class CArray
     # Create block iterator.
     def blocks (*args)